These analyses examine the relationship between expression levels and viral titer for a set of genes that we hypothesize have a relationship with viral infection. The overall strategy is to:

  1. Identify a list of candidate genes based on the literature and previous analyses.
  2. Subset our overall set of transcripts to include only those with an annotation containing the name of the candidate gene in the SwissProt gene name, SwissProt gene function, KEGG pathway, or EggNOG gene orthology annotations.
  3. Manually filter search results to remove non-target inclusions
  4. Remove transcripts with no variation in expression for each comparison (e.g., bursa at transcript-level)
  5. Use a linear mixed effects model to assess the relationship between log(expression) and log(viral titer) for each candidate gene/transcript. The model structure is expression ~ virus shedding group + sex + weight on day 55 + age with the sequencing pool as a random effect. The model is run on the entire set, as well as just on treatment groups I1, I3, I5, and I14.
  6. Correct the p-values for multiple testing using a false discovery rate approach with adjusted p-values (i.e., q-value) cutoff of 0.05. Corrections are used for just the test that incorporates all treatment groups because that is the only one used for filtering.
  7. Plot the results

Summarize results

identifier comparison Overall I1 I3 I5 I14
DN13777_c0_g1 BG 0.0000000 0.0002457 0.0000000 0.0000042 0.0306137
DN1920_c0_g1 BG 0.0001200 0.0423399 0.1784643 0.4778861 0.1915490
DN2085_c0_g2 BG 0.0001351 0.0357795 0.2492605 0.6274357 0.1063798
DN100201_c0_g1 IG 0.0005227 0.9749053 0.3054085 0.7895548 NA
DN110170_c0_g1 IG 0.0002874 0.1984860 0.0817690 0.5577861 NA
DN12243_c0_g1 IG 0.0006904 0.8054642 0.8925774 0.2239282 NA
DN12298_c0_g1 IG 0.0000065 0.6838584 0.7210650 0.9412309 NA
DN13002_c0_g1 IG 0.0007384 0.8474837 0.8501370 0.8085976 NA
DN13412_c0_g1 IG 0.0000966 0.0552989 0.5542637 0.2750548 NA
DN13777_c0_g1 IG 0.0000001 0.0012104 0.0006617 0.0000153 NA
DN1500_c0_g1 IG 0.0000001 0.0562891 0.0913101 0.1359571 NA
DN15121_c0_g1 IG 0.0000271 0.4598885 0.7630760 0.1431159 NA
DN15388_c0_g1 IG 0.0008409 0.1008436 0.6492697 0.2282883 NA
DN15488_c0_g1 IG 0.0013282 0.3472472 0.7348672 0.2947731 NA
DN15589_c0_g1 IG 0.0001027 0.8898813 0.5540308 0.6149295 NA
DN15963_c0_g1 IG 0.0017480 0.8112827 0.9109089 0.6533554 NA
DN161_c0_g1 IG 0.0001469 0.1013590 0.4409659 0.0680196 NA
DN1634_c0_g1 IG 0.0002114 0.0637586 0.5753947 0.3507569 NA
DN164_c3_g1 IG 0.0000000 0.0670560 0.5401402 0.0252898 NA
DN16598_c0_g1 IG 0.0001082 0.1915806 0.5307308 0.3791410 NA
DN17675_c0_g1 IG 0.0027248 0.6637614 0.2083687 0.0606560 NA
DN17675_c0_g2 IG 0.0003852 0.0553275 0.0753232 0.7042165 NA
DN178217_c0_g1 IG 0.0000890 0.1584390 0.6435868 0.8111403 NA
DN18052_c0_g1 IG 0.0000087 0.0181791 0.9708099 0.4705773 NA
DN186640_c0_g2 IG 0.0007748 0.7289134 0.6579285 0.7726904 NA
DN1920_c0_g1 IG 0.0000011 0.1570849 0.1803044 0.9783519 NA
DN1934_c0_g1 IG 0.0000001 0.1095985 0.6869747 0.4062469 NA
DN20116_c0_g1 IG 0.0004737 0.1242741 0.4350240 0.0330498 NA
DN2085_c0_g2 IG 0.0000008 0.1514934 0.5003724 0.1301007 NA
DN20874_c0_g1 IG 0.0000273 0.0795423 0.3356033 0.1773194 NA
DN24849_c0_g1 IG 0.0023869 0.2540017 0.2569959 0.5739374 NA
DN2578_c0_g1 IG 0.0016864 0.1861951 0.5844168 0.8446426 NA
DN2677_c0_g1 IG 0.0003549 0.2943114 0.5780663 0.3582156 NA
DN28958_c0_g1 IG 0.0000755 0.6277841 0.3321894 0.2417476 NA
DN2932_c0_g1 IG 0.0000000 0.0289823 0.7016237 0.0027597 NA
DN30475_c0_g1 IG 0.0004659 0.4762168 0.9857349 0.1768048 NA
DN3126_c0_g1 IG 0.0015378 0.3424404 0.4767143 0.9462094 NA
DN313_c0_g5 IG 0.0000715 0.4669163 0.8040424 0.2650549 NA
DN3236_c0_g1 IG 0.0000515 0.0319840 0.8350445 0.0438602 NA
DN4778_c0_g1 IG 0.0020781 0.3401251 0.9361751 0.6144636 NA
DN51353_c2_g1 IG 0.0017665 0.0070759 0.2975969 0.6792909 NA
DN5594_c0_g1 IG 0.0002156 0.1601010 0.4136610 0.9401905 NA
DN6170_c0_g1 IG 0.0000002 0.0399000 0.8807998 0.4861000 NA
DN6178_c0_g1 IG 0.0000001 0.0614417 0.5533242 0.5265663 NA
DN6190_c0_g1 IG 0.0000001 0.0452732 0.2803742 0.4124211 NA
DN71517_c0_g1 IG 0.0015885 0.1809656 0.7788231 0.6769996 NA
DN718_c0_g1 IG 0.0000679 0.0525693 0.4674214 0.5161730 NA
DN7889_c0_g1 IG 0.0005810 0.0250951 0.3423258 0.7062916 NA
DN7889_c0_g2 IG 0.0000004 0.1462079 0.5200290 0.4045887 NA
DN7919_c0_g1 IG 0.0006059 0.6703356 0.6805724 0.7941134 NA
DN7951_c0_g1 IG 0.0015212 0.9895003 0.8393424 0.3711901 NA
DN861_c0_g1 IG 0.0000414 0.2760121 0.8187034 0.9410730 NA
DN876_c0_g1 IG 0.0018933 0.0367493 0.2898880 0.0107654 NA
DN9204_c0_g1 IG 0.0005258 0.5734208 0.6286847 0.2146806 NA
DN100201_c0_g1_i1 IT 0.0006017 0.9674304 0.3054085 0.8112763 NA
DN110170_c0_g1_i1 IT 0.0007449 0.2450211 0.0851784 0.5501693 NA
DN12243_c0_g1_i2 IT 0.0009066 0.5666561 0.9201629 0.1707354 NA
DN12298_c0_g1_i2 IT 0.0000200 0.5585613 0.7334869 0.7758338 NA
DN13412_c0_g1_i3 IT 0.0003263 0.0791095 0.5730355 0.5008919 NA
DN1500_c0_g1_i13 IT 0.0000060 0.0443676 0.0986056 0.5951446 NA
DN1500_c0_g1_i23 IT 0.0005338 0.2044469 0.2753491 0.6905629 NA
DN15121_c0_g1_i1 IT 0.0000689 0.1962456 0.6626928 0.0820029 NA
DN15963_c0_g1_i8 IT 0.0006461 0.6451699 0.7308253 0.7927866 NA
DN161_c0_g1_i6 IT 0.0005114 0.0866424 0.4269787 0.8487848 NA
DN1634_c0_g1_i9 IT 0.0009815 0.0530048 0.6417156 0.4233216 NA
DN164_c3_g1_i7 IT 0.0001283 0.0112436 0.3557746 0.7359973 NA
DN16598_c0_g1_i1 IT 0.0002616 0.1681724 0.5928059 0.4671223 NA
DN17675_c0_g2_i1 IT 0.0004230 0.0443871 0.0768113 0.7787312 NA
DN178217_c0_g1_i1 IT 0.0001679 0.1653279 0.6241030 0.7523876 NA
DN18052_c0_g1_i2 IT 0.0000254 0.0576805 0.6712405 0.4929419 NA
DN1920_c0_g1_i1 IT 0.0004389 0.1755189 0.5712542 0.1208495 NA
DN1920_c0_g1_i11 IT 0.0000007 0.1225395 0.1629400 0.5320538 NA
DN1920_c0_g1_i9 IT 0.0000031 0.1791319 0.2258172 0.8080550 NA
DN1934_c0_g1_i11 IT 0.0000008 0.1197772 0.7910869 0.1992770 NA
DN1934_c0_g1_i16 IT 0.0000160 0.1547166 0.7869529 0.3196566 NA
DN1934_c0_g1_i9 IT 0.0006888 0.0053517 0.3137556 0.2952949 NA
DN2085_c0_g2_i1 IT 0.0000022 0.0258168 0.5067250 0.9225432 NA
DN2085_c0_g2_i10 IT 0.0000000 0.1469680 0.6951578 0.1828130 NA
DN2085_c0_g2_i11 IT 0.0000001 0.0757702 0.7381470 0.2987985 NA
DN2085_c0_g2_i12 IT 0.0000011 0.0665094 0.4441324 0.0709222 NA
DN2085_c0_g2_i13 IT 0.0000001 0.2719919 0.8115735 0.8178132 NA
DN2085_c0_g2_i14 IT 0.0000000 0.1335820 0.6011494 0.3572011 NA
DN2085_c0_g2_i15 IT 0.0000003 0.0128800 0.7510383 0.3316555 NA
DN2085_c0_g2_i16 IT 0.0000000 0.0622301 0.6056401 0.2004222 NA
DN2085_c0_g2_i5 IT 0.0000000 0.1237185 0.7713230 0.0115229 NA
DN2085_c0_g2_i6 IT 0.0000457 0.2987776 0.6502813 0.8457257 NA
DN20874_c0_g1_i10 IT 0.0000092 0.0238897 0.6225498 0.1961652 NA
DN20874_c0_g1_i11 IT 0.0000492 0.2422890 0.5541467 0.7623369 NA
DN20874_c0_g1_i9 IT 0.0000296 0.0759034 0.5307903 0.1381514 NA
DN22_c0_g1_i12 IT 0.0000013 0.0482762 0.7854753 0.2262876 NA
DN2413_c0_g1_i2 IT 0.0000017 0.0257637 0.8808974 0.0719210 NA
DN2413_c0_g1_i3 IT 0.0001899 0.2564221 0.4346577 0.7692713 NA
DN2413_c0_g1_i5 IT 0.0010927 0.1058918 0.4840810 0.1747186 NA
DN2413_c0_g1_i6 IT 0.0000167 0.0422212 0.9284121 0.1269559 NA
DN2413_c0_g1_i8 IT 0.0000580 0.0500572 0.5902414 0.3031879 NA
DN2578_c0_g1_i3 IT 0.0009392 0.6721047 0.2849367 0.0066887 NA
DN2677_c0_g1_i1 IT 0.0006272 0.1544390 0.7122285 0.9420768 NA
DN2932_c0_g1_i6 IT 0.0000000 0.0282077 0.6990247 0.0030637 NA
DN3126_c0_g1_i7 IT 0.0009677 0.2859608 0.1573966 0.1637234 NA
DN3236_c0_g1_i10 IT 0.0000205 0.0306410 0.8002553 0.1233674 NA
DN5594_c0_g1_i10 IT 0.0001347 0.1104761 0.5194052 0.9028494 NA
DN5715_c0_g1_i1 IT 0.0013943 0.2877885 0.3276287 0.2761559 NA
DN5715_c0_g1_i5 IT 0.0013669 0.7310052 0.4914441 0.4209879 NA
DN6170_c0_g1_i10 IT 0.0000008 0.0353510 0.9412486 0.7868131 NA
DN6170_c0_g1_i5 IT 0.0011263 0.0357089 0.4454178 0.2265390 NA
DN6178_c0_g1_i1 IT 0.0000000 0.0479127 0.6270861 0.6680755 NA
DN6190_c0_g1_i1 IT 0.0000002 0.0545784 0.0306346 0.8453586 NA
DN6190_c0_g1_i2 IT 0.0000004 0.0454582 0.8031861 0.3366820 NA
DN6190_c0_g1_i4 IT 0.0000001 0.0790922 0.3436061 0.4135104 NA
DN6305_c0_g1_i8 IT 0.0005501 0.3208664 0.7495739 0.3611646 NA
DN718_c0_g1_i1 IT 0.0001486 0.0422897 0.4828536 0.5906990 NA
DN718_c0_g1_i3 IT 0.0000426 0.2304292 0.8060709 0.6910036 NA
DN7919_c0_g1_i9 IT 0.0006137 0.3584506 0.7074663 0.9382848 NA
DN861_c0_g1_i1 IT 0.0000264 0.2618125 0.8401304 0.9633486 NA
DN9204_c0_g1_i7 IT 0.0007145 0.4484475 0.6809563 0.1762624 NA

Functions for analyzing and plotting data

Plotting significant results